Abstract Emergingevidencesuggeststhathumanmicrobiome,composedofcollectivegenomesofasmanyas100trillion microorganisms, could be mediating disease-leading causal pathways initiated by environmental toxicants or otherfactorssuchasdrugusage.Prenatalarsenicexposurethroughdrinkingwater,forexample,couldinitiate perturbationofgutmicrobiome,andtherefore,childrencouldinheritperturbedmicrobiomecompositioniftheir mothershavearsenicexposureduringperinatalperiod.Theunhealthymicrobiomecompositioncould,inturn, induce children?s asthma, infection and allergy which could explain that arsenic exposure during pregnancy is relatedtochildren?sinfection.Takentogether,arsenicexposurecouldbetheinitiationofcausalpathwaysleading tochildren?sinfectionthroughperturbedmother?smicrobiomebeingpassedtochildren.Therearemanyother possibleinitiationfactorssuchasdiet,genemutation,deliverymodeandantibioticsleadingtodifferentchildren?s health outcomes. These mediations could happen through changes in particular microbial taxa or though the perturbation of microbiome population structure. While high-throughput sequencing technologies can characterizethetaxonomiccompositionofmicrobiomeinunprecedenteddetail,noneoftheexistingmediation analysis methods is adequate enough to model the mediation effects of microbiome due to the unique challenging features of microbiome data. Therefore, there is an urgent need to have appropriate mediation analysismethodsinplaceforestimatingandtestingthemediationaleffectsofhumanmicrobiome.Toaddress theseissues,wewilldeveloptwogeneralmediationanalysisframeworkstoidentifymediationthroughchanges inindividualmicrobialtaxaandmodelmediationthoughtheperturbationofoverallmicrobiomecomposition.The models will be tested with extensive simulations and cross validations. An R package and an interactive web applicationwillbedevelopedformodelimplementations.Intherealstudyapplications,wewillquantifyandtest the mediation effects of infant gut microbiome and breast-milk microbiome in the relations between prenatal exposures (e.g., arsenic exposure, maternal diet) and childhood infections and allerg/atopy in the first year of lifeusingtherichdatafromthelargeongoinglongitudinalmolecularepidemiologicNewHampshireBirthCohort study.Withtheapplicationsoftheproposedmodelsinacysticfibrosis(CF)study,wewillexaminewhetherCF transmembrane conductance regulator gene mutations lay the biological foundation for patterns in the developingmicrobiomeinthegutthatareassociatedwithCFexacerbationonsetinnewbornchildrenwithCF. ByanalyzingthedatafromtheInfantGrowthandMicrobiomeStudy,wewillanswerthekeyquestionoftherole playedbygutmicrobiomeinassociatingearlyantibioticexposure,deliveringmodeandfeedingmodewithinfant weightgain.